After retrieving Jack from Purgatory, Commander Shepard gives her access to Cerberus's files aboard the Normandy. After the mission on Horizon, Kelly will tell Shepard at some point that Jack wants to see the Commander in her “hidey hole on the Engineering Deck”. Talk to Jack and she wants to blow the facility to pieces; Shepard can comment that attacking allies is a bad idea, but the facility was decommissioned after Jack’s escape.